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phase 4 and 6 with 0.5s up
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‎docs/HPC_GUIDE.md‎

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@@ -48,7 +48,7 @@ watch -n 10 "ls -1 results_JOBID | wc -l"
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# Fetching the results once the job is done
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scp -r kanagnostopoul@snellius.surf.nl:~/CSS_Project/results/phase6_18780164 / ./results/
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scp -r kanagnostopoul@snellius.surf.nl:~/CSS_Project/results/phase6_18824496/ ./results/
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```
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The jobscript template can be found in ```run_analysis.sh``` (default rome paritition).

‎docs/plots.md‎

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b. Legend at the bottom and shared if more than one plot
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1. Bifuractuion
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- zoomed out
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- zoomed in
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1. Bifuractuion (Mean population vs. prey death rate)
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- zoomed out (phase 1)
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- zoomed in (phase 1.5)
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2. Critical Point Power Law
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- At the critical point and away from the critical point (pick critical, subcritical, supercritical)

‎hpc_data/phase4.2_18824493/experiments.log‎

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2026-01-28 13:58:09,429 [INFO] ============================================================
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2026-01-28 13:58:09,430 [INFO] PREDATOR-PREY HYDRA EFFECT EXPERIMENTS
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2026-01-28 13:58:09,430 [INFO] ============================================================
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2026-01-28 13:58:09,430 [INFO] Phases: [4]
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2026-01-28 13:58:09,430 [INFO] Output: results/phase4_18824493
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2026-01-28 13:58:09,430 [INFO] Cores: 64
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2026-01-28 13:58:09,430 [INFO] Numba: ENABLED
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2026-01-28 13:58:09,430 [INFO]
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2026-01-28 13:58:09,430 [INFO] ============================================================
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2026-01-28 13:58:09,430 [INFO] PHASE 4
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2026-01-28 13:58:09,430 [INFO] ============================================================
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2026-01-28 13:58:09,430 [INFO] Estimated: 750 sims, ~0.0h on 64 cores (~1 core-hours)
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2026-01-28 13:58:09,431 [INFO] Dry run - skipping execution
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2026-01-28 13:58:09,431 [INFO]
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2026-01-28 13:58:09,431 [INFO] ============================================================
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2026-01-28 13:58:09,431 [INFO] EXPERIMENTS COMPLETE
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2026-01-28 13:58:09,431 [INFO] ============================================================
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2026-01-28 13:58:10,685 [INFO] ============================================================
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2026-01-28 13:58:10,685 [INFO] PREDATOR-PREY HYDRA EFFECT EXPERIMENTS
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2026-01-28 13:58:10,685 [INFO] ============================================================
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2026-01-28 13:58:10,685 [INFO] Phases: [4]
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2026-01-28 13:58:10,685 [INFO] Output: results/phase4_18824493
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2026-01-28 13:58:10,685 [INFO] Cores: 64
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2026-01-28 13:58:10,686 [INFO] Numba: ENABLED
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2026-01-28 13:58:10,686 [INFO]
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2026-01-28 13:58:10,686 [INFO] ============================================================
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2026-01-28 13:58:10,686 [INFO] PHASE 4
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2026-01-28 13:58:10,686 [INFO] ============================================================
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2026-01-28 13:58:10,686 [INFO] Estimated: 750 sims, ~0.0h on 64 cores (~1 core-hours)
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2026-01-28 13:58:16,772 [INFO] Phase 4: Full 4D Parameter Sweep
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2026-01-28 13:58:16,772 [INFO] Parameters: prey_birth, prey_death, pred_birth, pred_death
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2026-01-28 13:58:16,772 [INFO] Range: 0.0 to 1.0 (11 steps)
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2026-01-28 13:58:16,772 [INFO] Grid Size: 250
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2026-01-28 13:58:16,772 [INFO] Replicates: 10
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2026-01-28 13:58:17,596 [INFO] Total simulations: 100,000
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2026-01-28 14:02:33,079 [INFO] Phase 4 complete. Results: results/phase4_18824493/phase4_results.jsonl
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2026-01-28 14:02:33,216 [INFO] Phase 4 runtime: 4.4 minutes
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2026-01-28 14:02:33,216 [INFO]
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2026-01-28 14:02:33,216 [INFO] ============================================================
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2026-01-28 14:02:33,216 [INFO] EXPERIMENTS COMPLETE
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2026-01-28 14:02:33,216 [INFO] ============================================================

‎hpc_data/phase4.2_18824493/phase4_config.json‎

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{
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"prey_birth": 0.2,
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"predator_birth": 0.8,
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"critical_prey_birth": 0.2,
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"critical_prey_death": 0.947,
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"n_prey_birth": 15,
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"n_prey_death": 5,
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"predator_birth_values": [
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"n_replicates": 10,
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"warmup_steps": 500,
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"measurement_steps": 500,
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"save_timeseries": false,
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"timeseries_subsample": 10,
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"collect_pcf": false,
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"pcf_sample_rate": 0.2,
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"pcf_max_distance": 20.0,
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"min_density_for_analysis": 0.002,
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"perturbation_magnitude": 0.1,
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"n_jobs": 64
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}

‎hpc_data/phase4.2_18824493/phase4_metadata.json‎

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{
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"phase": 4,
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"description": "Global 4D Sensitivity Analysis",
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"sweep_values": [
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"parameters_varied": [
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],
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"n_sims": 100000,
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"timestamp": "2026-01-28 14:02:33",
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"config": {
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"prey_birth": 0.2,
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"synchronous": false,
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"min_density_for_analysis": 0.002,
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"perturbation_magnitude": 0.1,
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"n_jobs": 64
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}
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}

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